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Crystal Structure of the anti-human P-Cadherin Fab CQY684 in complex with human P-Cadherin(108-324)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZTF 6ZTF,6ZTB experimental model PDB 6ZTB 6ZTF,6ZTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M calcium acetate, 10% (w/v) PEG 8,000, 0.1M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.05 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.691 α = 90 b = 77.795 β = 90 c = 133.406 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M mirrors 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999990 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 72.49 100 0.199 0.216 0.995 7.97 6.714 105445 40.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 2.392 2.585 0.396 0.88 6.967
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6ZTF,6ZTB 2.1 72.49 105437 5273 99.95 0.1936 0.1921 0.2053 0.2208 0.2362 RANDOM 52.86
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 9.1882 4.0883 -13.2766
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.32 t_omega_torsion 3.58 t_angle_deg 1.18 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.32 t_omega_torsion 3.58 t_angle_deg 1.18 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9990 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 6
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction